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Old 01-09-2012, 10:26 AM   #3
hmortens
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Location: RTP

Join Date: Aug 2011
Posts: 12
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I am using Joe Pickrell's data (http://eqtl.uchicago.edu/RNA_Seq_data/), which I believe are single end reads, and have been running them as such using the following settings.

> time tophat -r 200 -p 14 -o tophat_out_s_1 /illumina/runs/data/bowtie_indexes/hg19.ebwt.zip_FILES/hg19 s_1_sequence.fastq

so, I have been working with s_1, s_3, s_5, and s_7. each from different samples/individual.
From your message, I would continue to run each seperately through tophat.
At the Cufflinks stage, do you prefer to cuffmerge, and then run cuffdiff, or some other set of steps?
many thanks!
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